Job ID = 6456414 SRX = SRX3404010 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:53:01 prefetch.2.10.7: 1) Downloading 'SRR6303487'... 2020-06-21T10:53:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:42 prefetch.2.10.7: 'SRR6303487' is valid 2020-06-21T10:54:42 prefetch.2.10.7: 1) 'SRR6303487' was downloaded successfully 2020-06-21T10:54:42 prefetch.2.10.7: 'SRR6303487' has 0 unresolved dependencies Read 25437957 spots for SRR6303487/SRR6303487.sra Written 25437957 spots for SRR6303487/SRR6303487.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:21 25437957 reads; of these: 25437957 (100.00%) were unpaired; of these: 804762 (3.16%) aligned 0 times 17929954 (70.49%) aligned exactly 1 time 6703241 (26.35%) aligned >1 times 96.84% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3098149 / 24633195 = 0.1258 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:09:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:06: 1000000 INFO @ Sun, 21 Jun 2020 20:09:11: 2000000 INFO @ Sun, 21 Jun 2020 20:09:16: 3000000 INFO @ Sun, 21 Jun 2020 20:09:21: 4000000 INFO @ Sun, 21 Jun 2020 20:09:26: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:09:30: 6000000 INFO @ Sun, 21 Jun 2020 20:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:09:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:35: 7000000 INFO @ Sun, 21 Jun 2020 20:09:37: 1000000 INFO @ Sun, 21 Jun 2020 20:09:40: 8000000 INFO @ Sun, 21 Jun 2020 20:09:42: 2000000 INFO @ Sun, 21 Jun 2020 20:09:45: 9000000 INFO @ Sun, 21 Jun 2020 20:09:48: 3000000 INFO @ Sun, 21 Jun 2020 20:09:50: 10000000 INFO @ Sun, 21 Jun 2020 20:09:54: 4000000 INFO @ Sun, 21 Jun 2020 20:09:55: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:09:59: 5000000 INFO @ Sun, 21 Jun 2020 20:10:00: 12000000 INFO @ Sun, 21 Jun 2020 20:10:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 20:10:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:05: 6000000 INFO @ Sun, 21 Jun 2020 20:10:05: 13000000 INFO @ Sun, 21 Jun 2020 20:10:07: 1000000 INFO @ Sun, 21 Jun 2020 20:10:10: 14000000 INFO @ Sun, 21 Jun 2020 20:10:11: 7000000 INFO @ Sun, 21 Jun 2020 20:10:13: 2000000 INFO @ Sun, 21 Jun 2020 20:10:16: 15000000 INFO @ Sun, 21 Jun 2020 20:10:16: 8000000 INFO @ Sun, 21 Jun 2020 20:10:18: 3000000 INFO @ Sun, 21 Jun 2020 20:10:21: 16000000 INFO @ Sun, 21 Jun 2020 20:10:22: 9000000 INFO @ Sun, 21 Jun 2020 20:10:24: 4000000 INFO @ Sun, 21 Jun 2020 20:10:26: 17000000 INFO @ Sun, 21 Jun 2020 20:10:28: 10000000 INFO @ Sun, 21 Jun 2020 20:10:30: 5000000 INFO @ Sun, 21 Jun 2020 20:10:31: 18000000 INFO @ Sun, 21 Jun 2020 20:10:34: 11000000 INFO @ Sun, 21 Jun 2020 20:10:36: 6000000 INFO @ Sun, 21 Jun 2020 20:10:36: 19000000 INFO @ Sun, 21 Jun 2020 20:10:39: 12000000 INFO @ Sun, 21 Jun 2020 20:10:41: 20000000 INFO @ Sun, 21 Jun 2020 20:10:42: 7000000 INFO @ Sun, 21 Jun 2020 20:10:45: 13000000 INFO @ Sun, 21 Jun 2020 20:10:47: 21000000 INFO @ Sun, 21 Jun 2020 20:10:47: 8000000 INFO @ Sun, 21 Jun 2020 20:10:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:50: #1 total tags in treatment: 21535046 INFO @ Sun, 21 Jun 2020 20:10:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:10:50: #1 tags after filtering in treatment: 21534988 INFO @ Sun, 21 Jun 2020 20:10:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:51: 14000000 INFO @ Sun, 21 Jun 2020 20:10:52: #2 number of paired peaks: 906 WARNING @ Sun, 21 Jun 2020 20:10:52: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sun, 21 Jun 2020 20:10:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:52: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:10:52: #2 alternative fragment length(s) may be 4,132,597 bps INFO @ Sun, 21 Jun 2020 20:10:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05_model.r INFO @ Sun, 21 Jun 2020 20:10:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:53: 9000000 INFO @ Sun, 21 Jun 2020 20:10:57: 15000000 INFO @ Sun, 21 Jun 2020 20:10:59: 10000000 INFO @ Sun, 21 Jun 2020 20:11:03: 16000000 INFO @ Sun, 21 Jun 2020 20:11:05: 11000000 INFO @ Sun, 21 Jun 2020 20:11:08: 17000000 INFO @ Sun, 21 Jun 2020 20:11:10: 12000000 INFO @ Sun, 21 Jun 2020 20:11:14: 18000000 INFO @ Sun, 21 Jun 2020 20:11:16: 13000000 INFO @ Sun, 21 Jun 2020 20:11:20: 19000000 INFO @ Sun, 21 Jun 2020 20:11:22: 14000000 INFO @ Sun, 21 Jun 2020 20:11:26: 20000000 INFO @ Sun, 21 Jun 2020 20:11:28: 15000000 INFO @ Sun, 21 Jun 2020 20:11:32: 21000000 INFO @ Sun, 21 Jun 2020 20:11:33: 16000000 INFO @ Sun, 21 Jun 2020 20:11:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:11:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:11:36: #1 total tags in treatment: 21535046 INFO @ Sun, 21 Jun 2020 20:11:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:11:36: #1 tags after filtering in treatment: 21534988 INFO @ Sun, 21 Jun 2020 20:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:38: #2 number of paired peaks: 906 WARNING @ Sun, 21 Jun 2020 20:11:38: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:38: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:11:38: #2 alternative fragment length(s) may be 4,132,597 bps INFO @ Sun, 21 Jun 2020 20:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10_model.r INFO @ Sun, 21 Jun 2020 20:11:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:39: 17000000 INFO @ Sun, 21 Jun 2020 20:11:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:45: 18000000 INFO @ Sun, 21 Jun 2020 20:11:50: 19000000 INFO @ Sun, 21 Jun 2020 20:11:56: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:02: 21000000 INFO @ Sun, 21 Jun 2020 20:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.05_summits.bed INFO @ Sun, 21 Jun 2020 20:12:04: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (4637 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:05: #1 total tags in treatment: 21535046 INFO @ Sun, 21 Jun 2020 20:12:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:12:06: #1 tags after filtering in treatment: 21534988 INFO @ Sun, 21 Jun 2020 20:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:08: #2 number of paired peaks: 906 WARNING @ Sun, 21 Jun 2020 20:12:08: Fewer paired peaks (906) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 906 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:08: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:12:08: #2 alternative fragment length(s) may be 4,132,597 bps INFO @ Sun, 21 Jun 2020 20:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20_model.r INFO @ Sun, 21 Jun 2020 20:12:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:51: Done! pass1 - making usageList (544 chroms): 2 millis pass2 - checking and writing primary data (3327 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:13:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404010/SRX3404010.20_summits.bed INFO @ Sun, 21 Jun 2020 20:13:20: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (2186 records, 4 fields): 16 millis CompletedMACS2peakCalling